Soil Health

Soil Testing with Microbial Density and Diversity (MDD) Analysis

Does your soil have the microbial populations it needs to support plant growth?


Microbial Density and Diversity (MDD) Analysis uses microscopy to estimate the density and diversity of fungi, bacteria, protists, and microarthropods in your soil.

These microbial populations help us determine whether your soil is supporting the active food webs that help your plants grow well with fewer inputs.

When rich and diverse food webs are working in your soil, yields increase, flavor and nutrition improves, and the need for chemical inputs is minimized or eliminated.

  • Frequently asked questions about MDD Analysis can be found here.


Prefer to do it yourself?

We also offer MDD Analysis Clinics, workshops, and online training.


Interested in hosting a Clinic or Workshop in your location?   Contact Us Here for details.

Why does soil need so many kinds of microbes?

Put simply, plants work best when microbes are present.  With more than a billion microbes in a teaspoon of healthy soil, it would be impossible to say what each indvidual does.  But the generalizations below should give you an idea about why diversity and density of soil microbial populations matter.

Bacteria (and Archaea) 

Although bacteria and archaea represent two distinct domains of prokaryotic  organisms, we lump them together in our assays, simply because you cannot tell them apart with the method we use.   If you need that kind of resolution, ask us about options for DNA analysis. Otherwise, simply remember that according to widely accepted geologic history bacteria and archaea preceeded all other life on earth by about a billion years.  This means that back in the day when our planet was nothing but a toxic wasteland of greenhouse gasses, it was the prokaryotes that cleaned the air, dissolved the minerals, and created the first foods necessary to support all other life forms.  Today, prokaryotes are the most abundant organisms on the planet, and because they are the first “autotrophs” (self-feeders)  they are the absolute “bottom” of the food chain. Without them, everything else suffers.

Prokaryotes are metabolic geniuses!  They can make any chemical, any medication, or any pesticide that you need to keep your soil and your food healthy and productive.  They also evolve faster than genes can be engineered, so when you have a healthy soil microbial population, there is no need to use the highly controversial, genetically modified crop plants (GMO’s).


Protists were the first eukaryotic cells.  They are believed to have evolved when an early prokaryote consumed another prokaryote, but could not digest it. We call this process endosymbiosis. Today, protists include large organisms like giant kelp (which can be a great source of plant nutrients).  But those protists that live in healthy soil  are the microscopic  algae, cilliates, amoeba, and  other wiggly, squiggly critters similar to things you saw under the microscope when you were in high school.  Sure, these protists look tiny to you.  But they are giants in a bacterial world!  Some protists fix carbon, just like plants do.  These are important for feeding bacteria at the soil surface.  Other protists consume hundreds of prokaryotes a day!  These are important for keeping prokaryote populations in check, much like a toad in your garden can keep insect populations under control. 


Think of fungi as the keystone species to healthy soils.   Much like the keystone at the apex of a masonry arch holds the entire arch together, fungi in the soil are key to health crop systems. 

Why?  Because fungi are the decomposers that eliminate waste and recycle nutrients.  But this is only the beginning.  Like the transportation and communication systems that bring food and health care to our cities, fungi serve as powerful resource networks underground.   These massive networks of transport tubes called hyphae connect plants to one another, and carry chemical messages and mineral nutrients from one plant to another. 

Plants grown in soils with healthy and diverse fungal populations tend to be nutrient dense, rich in flavor, and resistant to stress and disease.   On the other hand, plants grown in soils where fungal networks have been damaged by excessive tillage or chemical applications will require additional inputs in order to produce a reasonable crop.


We aren’t talking lions, tigers and bears, of course.  But there are dozens of tiny animals that thrive in a healthy soil.  Take for example this water bear.  Even a very low grade microscope can detect these guys!

Microscopic animals like nematodes, water bears, and microarthropods create holes (air vents) in your soil as they wander about.  These holes allow air and water into your soil.  Animals also eat other organisms, so they are good at keeping the bacteria, fungi, and even one another from becoming invasive.

Diversity matters!

Any microbe is capable of helping or hurting your plants.  When you have enough of them, they support plant growth.  When you have too many of any one kind, your system becomes diseased.   One key to keeping healthy soil is to have enough diversity in your soil life to ensure balance.

MDD analysis offers a low cost tool for confirming that your soil has sufficient  diversity and density to sustain an active, balanced, soil food web that keeps nutrients flowing into your plants, and protects your plants against stress, pests, and disease.